WIP: Add FsspecJsonWSIReader class.

[aacic]

The FsspecJsonWSIReader reads fsspec json file which represents SVS wsi.
The methods: read_rect, read_bounds, _canonical_shape are copied from TIFFWSIReader, and it needs to be improved by introducing delegates or some other way.

The method infor reads SVS metadata which is stored in the root group metadata like:

{
  ".zattrs": {
    "multiscales": [
      {
        "metadata": {
          "objective_power": 40,
          "vendor": "Aperio",
          "mpp": [0.2525, 0.2525]	
        }
      }
    ]
  }
}

To test, execute from the root dir:

pip install -r requirements/requirements_dev.txt
mkdir -p samples/slides
mkdir -p samples/fsspec
cd samples/slides
curl -C - -o TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs   https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27
cd ../../tests/zarrtiff/
python tiff_fsspec.py "../../samples/slides/TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs"  "../../samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json" "https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27"

Change the svs variable inside of tileserver.py to:

svs = "../../samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json"

python tileserver.py

Open http://127.0.0.1:5000/ and verify how it works.

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Codecov Report

Attention: Patch coverage is 72.58065% with 51 lines in your changes missing coverage. Please review.

Project coverage is 99.34%. Comparing base (d82df5c) to head (1ce4610).

Files with missing lines	Patch %	Lines
tiatoolbox/wsicore/wsireader.py	66.66%	46 Missing and 3 partials ⚠️
tiatoolbox/utils/tiff_to_fsspec.py	94.87%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #897      +/-   ##
===========================================
- Coverage    99.90%   99.34%   -0.57%     
===========================================
  Files           70       71       +1     
  Lines         8735     8852     +117     
  Branches      1149     1163      +14     
===========================================
+ Hits          8727     8794      +67     
- Misses           3       50      +47     
- Partials         5        8       +3     

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[shaneahmed]

Add a link to tiff-fsspec generator file.

[aacic]

The method is migrated to:
FsspecJsonWSIReader.is_valid_zarr_fsspec(file_path: str) -> bool:

I've extended the docs and added a link to tiff-to-fsspec generator file.

[shaneahmed]

Please change to appropriate name e.g., fsspecWSIReader.

[aacic]

Changed to FsspecJsonWSIReader.

[shaneahmed]

Add some documentation / introduction about the fsspec / json files.

[aacic]

Added documentation and the link to tiff_to_fsspec.py.

[shaneahmed]

It would be useful to add some description about why we need fsspec JSON file.

[aacic]

I've included a more detailed description and cleaned up the script.

I've working to bring the PR to the state when it's "Ready for review". It will require some more effort.